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PR00842

Identifier
GLHYDLASE14B  [View Relations]  [View Alignment]  
Accession
PR00842
No. of Motifs
7
Creation Date
11-MAR-1998  (UPDATE 07-JUN-1999)
Title
Plant beta-amylase signature
Database References
PRINTS; PR00750 BETAAMYLASE
INTERPRO; IPR001371
PDB; 1BTC
SCOP; 1BTC
CATH; 1BTC
Literature References
1. HENRISSAT, B.
A classification of glycosyl hydrolases based on amino acid sequence
similarities.
BIOCHEM.J. 280 309-316 (1991).
 
2. HENRISSAT, B. AND BAIROCH, A.
New families in the classification of glycosyl hydrolases based on amino 
acid sequence similarities.
BIOCHEM.J. 293 781-788 (1993).
 
3. HENRISSAT, B. AND BAIROCH, A.
Updating the sequence-based classification of glycosyl hydrolases.
BIOCHEM.J. 316 695-696 (1996).
 
4. EL HASSOUNI, M., HENRISSAT, B., CHIPPAUX, M. AND BARRAS, F.
Nucleotide sequences of the Arb genes, which control beta-glucosidase
utilisation in Erwinia chrysanthemi - Comparison with the Escherichia
coli Bgl operon and evidence for a new beta-glycohydrolase family
including enzymes from eubacteria, archaebacteria and humans.
J.BACTERIOL. 174 765-777 (1992).
 
5. VIKSONIELSEN, A., CHRISTENSEN, T.M., BOJKO, M. AND MARCUSSEN, J.
Purification and characterization of beta-amylase from leaves of potato
PHYSIOLOGIA PLANTARUM 99 190-196 (1997).
 
6. MIKAMI, B., SATO, M., SHIBATA, T., HIROSE, M., AIBARA, S., KATSUBE, Y.
AND MORITA, Y.
Three-dimensional structure of soybean beta-amylase determined at 3.0 A 
resolution: preliminary chain tracing of the complex with alpha-cyclodextrin. 
J.BIOCHEMISTRY 112 541-546 (1992). 

Documentation
O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that
hydrolyse the glycosidic bond between two or more carbohydrates, or between
a carbohydrate and a non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has led to the definition
of up to 60 different families [1-4] (http://expasy.hcuge.ch/cgi-bin/lists?
glycosid.txt). Family 14 (EC 3.2.1.2) encompasses the beta-amylase enzymes.
 
Beta-amylases, which are found in plants and bacteria, hydrolyse 1,4-alpha-
glucosidic linkages in starch-type polysaccharide substrates, removing
successive maltose units from the non-reducing ends of the chains [5]. In 
potato plants, the enzyme has been found to work optimally at 40 degrees C, 
becoming unstable above this temperature [5]. On the basis of sequence
comparisons, plant and bacterial beta-amylases can be readily distinguished
from each other. 
 
The 3D structure of a complex of soybean beta-amylase with an inhibitor 
(alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray
diffraction [6]. The enzyme folds into large and small domains: the large
domain has a (beta alpha)8 super-secondary structural core, while the smaller
is formed from two long loops extending from the beta-3 and beta-4 strands
of the (beta alpha)8 fold [6]. The interface of the two domains, together
with shorter loops from the (beta alpha)8 core, form a deep cleft, in which 
the inhibitor binds [6]. Two maltose molecules also bind in the cleft,
one sharing a binding site with alpha-cyclodextrin, and the other sitting
more deeply in the cleft [6].
 
GLHYDLASE14B is a 7-element fingerprint that provides a signature for
plant beta-amylases. The fingerprint was derived from an initial
alignment of 5 sequences: the motifs were drawn from conserved regions 
spanning the C-terminal half of the alignment, focusing on those regions
that characterise the plant beta-amylases but distinguish them from the rest
of the beta-amylase family - motif 1 includes beta-strand 8; motif 2 spans
helix 17; motif 3 spans the C-terminus of helix 20 and strand 11; motif 4
includes the N-terminus of helix 21; motif 6 spans the C-terminus of strand
12, helix 22 and the N-terminus of helix 23; motif 7 encodes the remainder
of helix 23. Two iterations on OWL30.0 were required to reach convergence,
at which point a true set comprising 15 sequences was identified. Two partial
matches were also found: AMYB_SECCE is a fragment from Secale cereale that
lacks the portion of sequence bearing motif 1; and AF012345 is a fragment
from Hordeum vulgare that matches motifs 2-5.
 
An update on SPTR37_9f identified a true set of 13 sequences.
Summary Information
13 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
713131313131313
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
AMYB_ARATH    AMYB_HORVU    AMYB_IPOBA    AMYB_MAIZE    
AMYB_MEDSA AMYB_SOYBN AMYB_TRIRP AMYB_VIGUN
AMYB_WHEAT Q08335 Q42795 Q42989
Q42990
Sequence Titles
AMYB_ARATH  BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
AMYB_HORVU BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - HORDEUM VULGARE (BARLEY).
AMYB_IPOBA BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - IPOMOEA BATATAS (SWEET POTATO) (BATATE).
AMYB_MAIZE BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - ZEA MAYS (MAIZE).
AMYB_MEDSA BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - MEDICAGO SATIVA (ALFALFA).
AMYB_SOYBN BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - GLYCINE MAX (SOYBEAN).
AMYB_TRIRP BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - TRIFOLIUM REPENS (CREEPING WHITE CLOVER).
AMYB_VIGUN BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - VIGNA UNGUICULATA (COWPEA).
AMYB_WHEAT BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - TRITICUM AESTIVUM (WHEAT).
Q08335 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - SECALE CEREALE (RYE).
Q42795 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - GLYCINE MAX (SOYBEAN).
Q42989 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - ORYZA SATIVA (RICE).
Q42990 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE) - ORYZA SATIVA (RICE).
Scan History
OWL30_3    2  75   NSINGLE    
SPTR37_9f 2 14 NSINGLE
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
GLIIDIEVGL AMYB_SOYBN 172 172 -
GDIVDIEVGC AMYB_IPOBA 173 173 -
GVVVDIEVGL AMYB_MAIZE 170 170 -
GVIVDIEVGL AMYB_HORVU 170 170 -
GVIVDIEVGL AMYB_ARATH 175 175 -

Motif 2 width=11
Element Seqn Id St Int Rpt
IARMLSRHHAI AMYB_SOYBN 328 146 -
IARMLARHHAT AMYB_IPOBA 330 147 -
IAHMLTRHRAS AMYB_MAIZE 326 146 -
IARMLKRHRAS AMYB_HORVU 326 146 -
IARMLSKHYGI AMYB_ARATH 331 146 -

Motif 3 width=10
Element Seqn Id St Int Rpt
GWREDIRVAG AMYB_SOYBN 370 31 -
GWKEYIDVAG AMYB_IPOBA 372 31 -
GWREGLNLAC AMYB_MAIZE 368 31 -
GWREGLNVAC AMYB_HORVU 368 31 -
AWKEGIEVAG AMYB_ARATH 373 31 -

Motif 4 width=10
Element Seqn Id St Int Rpt
PRYDATAYNQ AMYB_SOYBN 384 4 -
PRYDATAYNQ AMYB_IPOBA 386 4 -
NRYDATAYNT AMYB_MAIZE 382 4 -
PRYDPTAYNT AMYB_HORVU 382 4 -
ETYGAKGYNQ AMYB_ARATH 387 4 -

Motif 5 width=17
Element Seqn Id St Int Rpt
KPQGVNNNGPPKLSMFG AMYB_SOYBN 399 5 -
RPNGVNLNGPPKLKMSG AMYB_IPOBA 401 5 -
RPQGINKNGPPEHKLHG AMYB_MAIZE 397 5 -
RPHGINQSGPPEHKLFG AMYB_HORVU 397 5 -
RPNGVNPNGKPKLRMYG AMYB_ARATH 402 5 -

Motif 6 width=15
Element Seqn Id St Int Rpt
TYLRLSDDLLQKSNF AMYB_SOYBN 417 1 -
TYLRLSDDLLQTDNF AMYB_IPOBA 419 1 -
TYLRVSDELFQEQNY AMYB_MAIZE 415 1 -
TYLRLSNQLVEGQNY AMYB_HORVU 415 1 -
TYLRLSDTVFQENNF AMYB_ARATH 420 1 -

Motif 7 width=15
Element Seqn Id St Int Rpt
NIFKKFVLKMHADQD AMYB_SOYBN 432 0 -
ELFKKFVKKMHADLD AMYB_IPOBA 434 0 -
TTFKTFVRRMHANLD AMYB_MAIZE 430 0 -
VNFKTFVDRMHANLP AMYB_HORVU 430 0 -
ELFKKLVRKMHADQD AMYB_ARATH 435 0 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
GLIIDIEVGL Q42795 173 173 -
GVIVDIEVGL Q42989 170 170 -
GVIVDIEVGL Q42990 170 170 -
GLIIDIEVGL AMYB_SOYBN 172 172 -
GTIVDIEVGL AMYB_WHEAT 170 170 -
EVIIDIEVGL AMYB_VIGUN 173 173 -
GTIVDIEVGL Q08335 170 170 -
EVIIDIEVGL AMYB_MEDSA 173 173 -
ELIIDIEVGL AMYB_TRIRP 173 173 -
GDIVDIEVGC AMYB_IPOBA 173 173 -
GVVVDIEVGL AMYB_MAIZE 170 170 -
GVIVDIEVGL AMYB_HORVU 170 170 -
GVIVDIEVGL AMYB_ARATH 175 175 -

Motif 2 width=11
Element Seqn Id St Int Rpt
IARMLSRHHAI Q42795 329 146 -
IARMLTRHRAC Q42989 326 146 -
IARMLTRHRAC Q42990 326 146 -
IARMLSRHHAI AMYB_SOYBN 328 146 -
IARMLTRHHAS AMYB_WHEAT 326 146 -
IAKMVSRHHAS AMYB_VIGUN 329 146 -
IARMLTRHHAS Q08335 326 146 -
IAKIVSRHHAI AMYB_MEDSA 329 146 -
IAKMVSRHHGI AMYB_TRIRP 329 146 -
IARMLARHHAT AMYB_IPOBA 330 147 -
IAHMLTRHRAS AMYB_MAIZE 326 146 -
IARMLKRHRAS AMYB_HORVU 326 146 -
IARMLSKHYGI AMYB_ARATH 331 146 -

Motif 3 width=10
Element Seqn Id St Int Rpt
GWREDIRVAG Q42795 371 31 -
GWREGLHVAC Q42989 368 31 -
GWREGLHVAC Q42990 368 31 -
GWREDIRVAG AMYB_SOYBN 370 31 -
GWREGLHVAC AMYB_WHEAT 368 31 -
GWRENIEVAG AMYB_VIGUN 371 31 -
GWREGLHVAC Q08335 368 31 -
GWRENIEVAG AMYB_MEDSA 371 31 -
GWRENIEVAG AMYB_TRIRP 371 31 -
GWKEYIDVAG AMYB_IPOBA 372 31 -
GWREGLNLAC AMYB_MAIZE 368 31 -
GWREGLNVAC AMYB_HORVU 368 31 -
AWKEGIEVAG AMYB_ARATH 373 31 -

Motif 4 width=10
Element Seqn Id St Int Rpt
PRYDATAYNQ Q42795 385 4 -
GRYDATAYNT Q42989 382 4 -
GRYDATAYNT Q42990 382 4 -
PRYDATAYNQ AMYB_SOYBN 384 4 -
GRYDATAYNT AMYB_WHEAT 382 4 -
SRYDATAYNQ AMYB_VIGUN 385 4 -
GRYDATAYNT Q08335 382 4 -
SRYDATAYNQ AMYB_MEDSA 385 4 -
SRYDATAYNQ AMYB_TRIRP 385 4 -
PRYDATAYNQ AMYB_IPOBA 386 4 -
NRYDATAYNT AMYB_MAIZE 382 4 -
PRYDPTAYNT AMYB_HORVU 382 4 -
ETYGAKGYNQ AMYB_ARATH 387 4 -

Motif 5 width=17
Element Seqn Id St Int Rpt
RPQGVNNNGPPKLSMFG Q42795 400 5 -
RPHGINKNGPPEHKLFG Q42989 397 5 -
RPHGINKNGPPEYKLFG Q42990 397 5 -
KPQGVNNNGPPKLSMFG AMYB_SOYBN 399 5 -
RPKGINKNGPPEHKLFG AMYB_WHEAT 397 5 -
RPQGVNKDGPPKHRMYG AMYB_VIGUN 400 5 -
RPKGINENGPPQHKLYG Q08335 397 5 -
RPQGVNKDGPPKLRMYG AMYB_MEDSA 400 5 -
RPQGVNKDGPPKLRMYG AMYB_TRIRP 400 5 -
RPNGVNLNGPPKLKMSG AMYB_IPOBA 401 5 -
RPQGINKNGPPEHKLHG AMYB_MAIZE 397 5 -
RPHGINQSGPPEHKLFG AMYB_HORVU 397 5 -
RPNGVNPNGKPKLRMYG AMYB_ARATH 402 5 -

Motif 6 width=15
Element Seqn Id St Int Rpt
TYLRLSDDLLQKSNF Q42795 418 1 -
TYLRLSDELLEGQNY Q42989 415 1 -
TYLRLSDELLEGQNY Q42990 415 1 -
TYLRLSDDLLQKSNF AMYB_SOYBN 417 1 -
TYLRLSNELLEGQNY AMYB_WHEAT 415 1 -
TYLRLSDELLQQSNF AMYB_VIGUN 418 1 -
TYLRLSNELQEGQNY Q08335 415 1 -
TYLRLSDDLMQQSNF AMYB_MEDSA 418 1 -
TYLRLSDDLLQESNF AMYB_TRIRP 418 1 -
TYLRLSDDLLQTDNF AMYB_IPOBA 419 1 -
TYLRVSDELFQEQNY AMYB_MAIZE 415 1 -
TYLRLSNQLVEGQNY AMYB_HORVU 415 1 -
TYLRLSDTVFQENNF AMYB_ARATH 420 1 -

Motif 7 width=15
Element Seqn Id St Int Rpt
NIFKKFVLKMHADQD Q42795 433 0 -
STFKTFVKRMHANLV Q42989 430 0 -
STFKTFVKRMHANLV Q42990 430 0 -
NIFKKFVLKMHADQD AMYB_SOYBN 432 0 -
ATFQTFVEKMHANLG AMYB_WHEAT 430 0 -
DIFKKFVVKMHADQD AMYB_VIGUN 433 0 -
ATFQTFVEKMHANLG Q08335 430 0 -
DIFKKFVVKMHADQD AMYB_MEDSA 433 0 -
EIFKKFVVKMHADQS AMYB_TRIRP 433 0 -
ELFKKFVKKMHADLD AMYB_IPOBA 434 0 -
TTFKTFVRRMHANLD AMYB_MAIZE 430 0 -
VNFKTFVDRMHANLP AMYB_HORVU 430 0 -
ELFKKLVRKMHADQD AMYB_ARATH 435 0 -